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I follow the steps; I just don't understand why they're treated as dispositive evidence of zoonosis. I also don't think you're correctly describing Bloom's posi
by tripletao 4y ago
I follow the steps; I just don't understand why they're treated as dispositive evidence of zoonosis. I also don't think you're correctly describing Bloom's position here. On Twitter, he writes:
> But the first sequences reported by Chinese government are lineage B from seafood market. So either outbreak was not seeded by lineage B at market, or something very complicated happened. I suggest the former, Pekar et al suggest the latter.
https://mobile.twitter.com/jbloom_lab/status/1534632834568052736 https://mobile.twitter.com/jbloom_lab/status/153463283456805...
I'm taking this as a statement that he disagrees with Pekar, and believes SARS-CoV-2 probably originated from a single introduction (natural or otherwise) into humans. That seems well beyond "slightly less likely". Am I mistaken?
Pekar's theory makes sense if we believe that sampling in humans has been almost perfectly good, capturing every important lineage. But why would we assume that? Such confidence in the human sampling is particularly odd when Pekar's theory also requires us to believe that sampling in animals has been perfectly bad, since we've still found no animals infected (except those infected by humans).
Assuming that Lineage A evolved into Lineage B in humans, the hidden ancestors don't need to be less pathogenic than SARS-CoV-2; the IFR is relatively low already, and people die of similar respiratory diseases every day. The novel virus wasn't discovered until mortality became alarmingly high, leaving lots of room for undiagnosed deaths from cryptic spread before that.
> Guo found environmental samples of both Lineage A and Lineage B at the market -- so both were present there -- his second hypothetical would then be highly unlikely.
Why does that make his second hypothetical highly unlikely? I don't understand why two zoonotic introductions into the market are more likely than two human introductions into the market. Perhaps you'd expect to see other sparks thrown off from the cryptic human spread; but almost all chains of transmission die out, with highly stochastic spread until enough people get infected for the central limit theorem to take over. So the absence of intermediate lineages doesn't seem too significant to me, especially when the "missing link" (if it even exists; I'll again note the lineages could have formed in a single human-to-human transmission) is literally just a single SNP from either lineage.